[Freesurfer] SNR on DTI data

c SNR values, I just need SNR for the whole DTI data for each group. Any suggestions will be appreciated! Yuko Yotsumoto --- - Yuko Yotsumoto, Ph. D. Associate Professor The University of Tokyo, Department of Life Sciences Bldg #2,

[Freesurfer] ADC, Radial diffusivity, Axial diffusivity and thresholds

, just average the values within a ROI. [2] Use some arbitrary thresholds to each of ADC, RD, AD. [3] create a mask that contains voxels of the above-threshold-FAvalues, then, calculate mean within the mask. Any suggestions? Best, Yuko Yotsumoto

Re: [Freesurfer] SNR on DTI data

in the white matter aseg mask? Thank you in advance! Yuko Yotsumoto Mar 18, 2014 1:26 PM、Anastasia Yendiki のメール： > > Signal-to-noise ratio = mean / standard deviation > > On Tue, 18 Mar 2014, Yuko Yotsumoto wrote: > >> Anastasia, >> >> Thank you so much f

[Freesurfer] DTI directions and slice angulation

using the correction. I'd appreciate any comments/suggestions. Thank you, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended

[Freesurfer] How to avoid overlaps between volume labels?

never share any voxels. What would be the best way to do so? Is there anything I can do using a command line? Best, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to avoid overlaps between volume labels?

Thank you all for your suggestions. I binarized my labels, used mri_concat --max, then re-binarize the volumes. It worked great. Thanks again, Yuko Yotsumoto On Jun 7, 2012, at 6:58 AM, Douglas Greve wrote: > It depends on how graceful you want to be with resolving the overlap. > One

[Freesurfer] registering functional labels to another anatomical data

ain A. Is there a way to convert the functional labels from Brain A to Brain B? Or do I need to re-do the whole functional analysis using the Brain B? Best, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] dt_recon error

les dt_recon.log dwi-ec.ecclog dwi-ec.nii dwi-infodump.dat dwi.nii mri_glmfit.log In dwi-infodump.dat, I see bunch of lines, but I don't see "sWiPMemBlock.alFree". Please help! Thanks, Yuko Yotsumoto #@#--- Fitting Tensors Wed Dec 7 10:15:52 JST 2011

Re: [Freesurfer] mri_glmfit-sim error with v5.0

I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? > When I paste "mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm > --surface fsaverage lh --glmdir MPglm.wls --nii.gz" in the command line, it > works without any error. > > Thanks in advan

Re: [Freesurfer] dt_recon error

> Hi Yuko, your dicom file might be from a different versioned scanner than > dt_recon is used to seeing. If so, then it cannot extract the bvecs and > bvals. If you supply them in a file on the command line, it should run > properly. > doug > > Yuko Yotsumoto wrote: >&

Re: [Freesurfer] dt_recon error

'll have to create text files of the bval/bvecs. The expected format > is given in the help. You'll have to ask someone who knows about your > sequences as to what the actual values you should use. > doug > > On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: >> Hi Doug, >

Re: [Freesurfer] dt_recon error

Doug, Never mind. I think I just figured it out!0 Yuko On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote: > Thanks Doug, > > In the dt_recon help, > >> The bvalues are in a simple text file, one for each direction >> (including b=0). The bvectors (gradient d

Re: [Freesurfer] dt_recon error

he help. You'll have to ask someone who knows about your > sequences as to what the actual values you should use. > doug > > On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: >> Hi Doug, >> >> Thank you for your reply. >>> If so, then it cannot extract the bve

[Freesurfer] func2roi-sess question : label2mask_linear: there were 0 label hits

this analysis, though I see clear activation within this label during task. Please let me know what I need to add/change to make func2roi-sess work. Thank you! Yuko Yotsumoto ### fucn2roi-sess log file $Id: func2roi-sess,v 1.16 2010/03/25 16:22:53

Re: [Freesurfer] func2roi-sess question : label2mask_linear: there were 0 label hits

s /subjects/self/surf/, which I don't have in my subject folder... Yuko Yotsumoto # log > [Yukos-iMac:sessions/VM/VMan] yuko% funcroi-sess -roi lh.DLPFC.roicfg -df > sessdirfile -s VM20 > --- > /Users/yuko/Documents/FreeSurfer/session

[Freesurfer] funcroi-table-sess

Hi All, I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd like to plot HDR for each condition for each subject. With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess. With v5.0, those commands do not seem to work. I could get a table with: > funcroi-config -anal

Re: [Freesurfer] funcroi-table-sess

oi-table-sess for each time point (using the -frame option), then > construct the waveforms from these files. It's a bit of a hassle, but > scriptable. > > doug > > Yuko Yotsumoto wrote: >> Hi All, >> >> I'm using : freesurfer-Darwin-leopard-i686-

[Freesurfer] funcroi-table-sess: average baseline activity?

Hi all, I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I've posted two questions (Q1 & Q2 below) in my previous email regarding ROI analysis, and I'd like to add one more (Q3). Q1) If I don't want to use any thresholding for ROI analysis, can I use "-sign abs -thresh 0" with funcr

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Thanks Doug, On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote: >> I'm using: >> freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 >> >> Q1) >> If I don't want to use any thresholding for ROI analysis, can I use "-sign >> abs -thresh 0" with funcroi-config? >> > Even easier: just don't specif

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

/funcroi-table-sess > > I've updated the docs for this one as well. > > thanks > > doug > > > Yuko Yotsumoto wrote: >> Thanks Doug, >> >> On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote: >> >> >>>> I'm using: >&

[Freesurfer] mkanalysis-sess and -TER

Hi all, ( freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 ) I created sequences for event-related design, using optseq2. optseq2 --ntp 150 --tr 2 --psdwin 0 20 1 --ev TG1 2 22 --ev IG1 2 22 --ev CNT 2 22 --ev TGIG 2 22 --ev TGCN 2 22 --nsearch 2000 --focb nCB10pt --nkeep 15 --o

[Freesurfer] freesurfer 4.5 download

Hi, I'm trying to download freesurfer 4.5 for leopard-ppc, but connection keeps failing. Could someone check the link? http://www.freesurfer.net/pub/dist/freesurfer/4.5.0/ Thank you, Yuko Yotsumoto ___ Freesurfer mailing list Frees

[Freesurfer] parametric modulator with FS-FAST

s with SPM, but I'd like to do this with FS-FAST. I found this post in the archive, but I need some more info. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14181.html Thanks! Yuko Yotsumoto --- Yuko Yotsumoto, Ph. D. Associate Professor T

[Freesurfer] Rejoindre mon réseau sur LinkedIn

LinkedIn Yuko Yotsumoto souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Yuko Yotsumoto http://www.linkedin.